
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms   40 (  160),  selected   40 , name T0349AL381_3-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349AL381_3-D1.T0349_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      R       2           -
LGA    -       -      E       3           -
LGA    -       -      L       4           -
LGA    -       -      L       5           -
LGA    -       -      R       6           -
LGA    -       -      T       7           -
LGA    -       -      N       8           -
LGA    -       -      D       9           -
LGA    -       -      A      10           -
LGA    -       -      V      11           -
LGA    L      12      L      12          0.918
LGA    L      13      L      13          1.891
LGA    S      14      S      14          1.743
LGA    A      15      A      15          0.716
LGA    V      16      V      16          0.567
LGA    G      17      G      17          1.234
LGA    A      18      A      18          0.889
LGA    L      19      L      19          0.666
LGA    L      20      L      20          0.984
LGA    D      21      D      21          0.892
LGA    G      22      G      22          0.486
LGA    A      23      A      23          1.653
LGA    D      24      D      24          2.118
LGA    I      25      I      25          0.837
LGA    G      26      G      26          1.880
LGA    -       -      H      27           -
LGA    -       -      L      28           -
LGA    V      29      V      29          4.694
LGA    R      46      P      45          3.799
LGA    -       -      R      46           -
LGA    R      47      R      47          0.193
LGA    V      48      V      48          0.682
LGA    L      49      L      49          0.910
LGA    V      50      V      50          0.901
LGA    H      51      H      51          1.092
LGA    E      52      E      52          1.449
LGA    D      53      D      53          1.435
LGA    D      54      D      54          1.209
LGA    L      55      L      55          0.289
LGA    A      56      A      56          0.676
LGA    G      57      G      57          0.600
LGA    A      58      A      58          0.373
LGA    R      59      R      59          0.574
LGA    R      60      R      60          0.524
LGA    L      61      L      61          0.195
LGA    L      62      L      62          0.458
LGA    T      63      T      63          0.584
LGA    D      64      D      64          0.788
LGA    A      65      A      65          2.523
LGA    -       -      G      66           -
LGA    G      66      L      67          1.981
LGA    L      67      A      68          2.707
LGA    A      68      H      69          2.974
LGA    H      69      E      70          6.110
LGA    -       -      L      71           -
LGA    -       -      R      72           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   40   57    5.0     40    1.85    87.50     64.781     2.054

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.655091 * X  +  -0.641385 * Y  +   0.399349 * Z  +   7.273233
  Y_new =   0.714359 * X  +   0.697925 * Y  +  -0.050910 * Z  + -63.138306
  Z_new =  -0.246063 * X  +   0.318630 * Y  +   0.915384 * Z  + -45.544365 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.334966   -2.806627  [ DEG:    19.1921   -160.8079 ]
  Theta =   0.248616    2.892976  [ DEG:    14.2447    165.7553 ]
  Phi   =   0.828649   -2.312943  [ DEG:    47.4781   -132.5219 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0349AL381_3-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349AL381_3-D1.T0349_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   40   57   5.0   40   1.85   87.50  64.781
REMARK  ---------------------------------------------------------- 
MOLECULE T0349AL381_3-D1
REMARK Aligment from pdb entry: 1yj7A
ATOM      1  N   LEU    12      -2.236  -4.459   7.361  1.00  0.00              
ATOM      2  CA  LEU    12      -1.205  -3.444   7.537  1.00  0.00              
ATOM      3  C   LEU    12      -1.460  -2.213   6.658  1.00  0.00              
ATOM      4  O   LEU    12      -1.265  -1.092   7.122  1.00  0.00              
ATOM      5  N   LEU    13      -1.892  -2.404   5.413  1.00  0.00              
ATOM      6  CA  LEU    13      -2.241  -1.264   4.573  1.00  0.00              
ATOM      7  C   LEU    13      -3.331  -0.468   5.269  1.00  0.00              
ATOM      8  O   LEU    13      -3.294   0.750   5.256  1.00  0.00              
ATOM      9  N   SER    14      -4.317  -1.146   5.867  1.00  0.00              
ATOM     10  CA  SER    14      -5.359  -0.432   6.596  1.00  0.00              
ATOM     11  C   SER    14      -4.836   0.373   7.776  1.00  0.00              
ATOM     12  O   SER    14      -5.273   1.493   8.001  1.00  0.00              
ATOM     13  N   ALA    15      -3.903  -0.201   8.522  1.00  0.00              
ATOM     14  CA  ALA    15      -3.311   0.497   9.652  1.00  0.00              
ATOM     15  C   ALA    15      -2.559   1.747   9.172  1.00  0.00              
ATOM     16  O   ALA    15      -2.702   2.827   9.739  1.00  0.00              
ATOM     17  N   VAL    16      -1.804   1.598   8.102  1.00  0.00              
ATOM     18  CA  VAL    16      -1.024   2.706   7.538  1.00  0.00              
ATOM     19  C   VAL    16      -1.923   3.799   6.946  1.00  0.00              
ATOM     20  O   VAL    16      -1.665   4.999   7.133  1.00  0.00              
ATOM     21  N   GLY    17      -2.976   3.386   6.227  1.00  0.00              
ATOM     22  CA  GLY    17      -3.927   4.307   5.621  1.00  0.00              
ATOM     23  C   GLY    17      -4.672   5.092   6.692  1.00  0.00              
ATOM     24  O   GLY    17      -4.782   6.314   6.621  1.00  0.00              
ATOM     25  N   ALA    18      -5.137   4.409   7.734  1.00  0.00              
ATOM     26  CA  ALA    18      -5.830   5.099   8.812  1.00  0.00              
ATOM     27  C   ALA    18      -4.898   6.044   9.569  1.00  0.00              
ATOM     28  O   ALA    18      -5.297   7.144   9.924  1.00  0.00              
ATOM     29  N   LEU    19      -3.651   5.636   9.790  1.00  0.00              
ATOM     30  CA  LEU    19      -2.672   6.491  10.440  1.00  0.00              
ATOM     31  C   LEU    19      -2.435   7.796   9.660  1.00  0.00              
ATOM     32  O   LEU    19      -2.412   8.888  10.225  1.00  0.00              
ATOM     33  N   LEU    20      -2.264   7.670   8.352  1.00  0.00              
ATOM     34  CA  LEU    20      -2.034   8.841   7.499  1.00  0.00              
ATOM     35  C   LEU    20      -3.255   9.734   7.488  1.00  0.00              
ATOM     36  O   LEU    20      -3.143  10.944   7.712  1.00  0.00              
ATOM     37  N   ASP    21      -4.436   9.165   7.255  1.00  0.00              
ATOM     38  CA  ASP    21      -5.634   9.990   7.201  1.00  0.00              
ATOM     39  C   ASP    21      -5.845  10.726   8.523  1.00  0.00              
ATOM     40  O   ASP    21      -6.221  11.895   8.539  1.00  0.00              
ATOM     41  N   GLY    22      -5.577  10.055   9.637  1.00  0.00              
ATOM     42  CA  GLY    22      -5.841  10.670  10.939  1.00  0.00              
ATOM     43  C   GLY    22      -4.797  11.727  11.305  1.00  0.00              
ATOM     44  O   GLY    22      -5.022  12.543  12.205  1.00  0.00              
ATOM     45  N   ALA    23      -3.684  11.730  10.574  1.00  0.00              
ATOM     46  CA  ALA    23      -2.634  12.722  10.680  1.00  0.00              
ATOM     47  C   ALA    23      -2.647  13.696   9.478  1.00  0.00              
ATOM     48  O   ALA    23      -1.625  14.287   9.102  1.00  0.00              
ATOM     49  N   ASP    24      -3.821  13.832   8.876  1.00  0.00              
ATOM     50  CA  ASP    24      -4.095  14.847   7.866  1.00  0.00              
ATOM     51  C   ASP    24      -3.205  14.745   6.635  1.00  0.00              
ATOM     52  O   ASP    24      -2.751  15.741   6.060  1.00  0.00              
ATOM     53  N   ILE    25      -3.017  13.507   6.197  1.00  0.00              
ATOM     54  CA  ILE    25      -2.433  13.208   4.904  1.00  0.00              
ATOM     55  C   ILE    25      -3.380  12.322   4.106  1.00  0.00              
ATOM     56  O   ILE    25      -3.733  11.218   4.536  1.00  0.00              
ATOM     57  N   GLY    26      -3.786  12.806   2.934  1.00  0.00              
ATOM     58  CA  GLY    26      -4.601  12.030   2.013  1.00  0.00              
ATOM     59  C   GLY    26      -3.847  10.808   1.525  1.00  0.00              
ATOM     60  O   GLY    26      -2.631  10.845   1.395  1.00  0.00              
ATOM     61  N   VAL    29      -4.777   0.729  -3.738  1.00  0.00              
ATOM     62  CA  VAL    29      -5.208  -0.209  -4.777  1.00  0.00              
ATOM     63  C   VAL    29      -4.719  -1.615  -4.453  1.00  0.00              
ATOM     64  O   VAL    29      -3.779  -1.782  -3.700  1.00  0.00              
ATOM     89  N   ARG    46      -1.615  -5.040  -1.400  1.00  0.00              
ATOM     90  CA  ARG    46      -2.097  -3.669  -1.374  1.00  0.00              
ATOM     91  C   ARG    46      -0.972  -2.676  -1.606  1.00  0.00              
ATOM     92  O   ARG    46       0.139  -2.865  -1.124  1.00  0.00              
ATOM     93  N   ARG    47      -1.292  -1.630  -2.360  1.00  0.00              
ATOM     94  CA  ARG    47      -0.390  -0.521  -2.636  1.00  0.00              
ATOM     95  C   ARG    47      -1.000   0.764  -2.095  1.00  0.00              
ATOM     96  O   ARG    47      -2.177   1.038  -2.324  1.00  0.00              
ATOM     97  N   VAL    48      -0.205   1.548  -1.368  1.00  0.00              
ATOM     98  CA  VAL    48      -0.619   2.854  -0.877  1.00  0.00              
ATOM     99  C   VAL    48       0.189   3.915  -1.595  1.00  0.00              
ATOM    100  O   VAL    48       1.395   3.756  -1.786  1.00  0.00              
ATOM    101  N   LEU    49      -0.493   4.978  -2.009  1.00  0.00              
ATOM    102  CA  LEU    49       0.100   6.144  -2.670  1.00  0.00              
ATOM    103  C   LEU    49      -0.381   7.432  -2.021  1.00  0.00              
ATOM    104  O   LEU    49      -1.407   7.446  -1.346  1.00  0.00              
ATOM    105  N   VAL    50       0.347   8.517  -2.251  1.00  0.00              
ATOM    106  CA  VAL    50      -0.053   9.843  -1.809  1.00  0.00              
ATOM    107  C   VAL    50       0.138  10.838  -2.952  1.00  0.00              
ATOM    108  O   VAL    50       0.816  10.553  -3.934  1.00  0.00              
ATOM    109  N   HIS    51      -0.451  12.014  -2.808  1.00  0.00              
ATOM    110  CA  HIS    51      -0.142  13.116  -3.713  1.00  0.00              
ATOM    111  C   HIS    51       1.337  13.401  -3.559  1.00  0.00              
ATOM    112  O   HIS    51       1.878  13.336  -2.441  1.00  0.00              
ATOM    113  N   GLU    52       2.031  13.681  -4.664  1.00  0.00              
ATOM    114  CA  GLU    52       3.488  13.818  -4.597  1.00  0.00              
ATOM    115  C   GLU    52       3.976  14.850  -3.595  1.00  0.00              
ATOM    116  O   GLU    52       5.015  14.649  -2.968  1.00  0.00              
ATOM    117  N   ASP    53       3.230  15.942  -3.424  1.00  0.00              
ATOM    118  CA  ASP    53       3.622  17.023  -2.547  1.00  0.00              
ATOM    119  C   ASP    53       3.613  16.587  -1.092  1.00  0.00              
ATOM    120  O   ASP    53       4.275  17.203  -0.263  1.00  0.00              
ATOM    121  N   ASP    54       2.876  15.520  -0.805  1.00  0.00              
ATOM    122  CA  ASP    54       2.718  15.015   0.553  1.00  0.00              
ATOM    123  C   ASP    54       3.713  13.906   0.910  1.00  0.00              
ATOM    124  O   ASP    54       3.655  13.342   2.021  1.00  0.00              
ATOM    125  N   LEU    55       4.624  13.579  -0.009  1.00  0.00              
ATOM    126  CA  LEU    55       5.470  12.416   0.180  1.00  0.00              
ATOM    127  C   LEU    55       6.330  12.508   1.458  1.00  0.00              
ATOM    128  O   LEU    55       6.381  11.557   2.243  1.00  0.00              
ATOM    129  N   ALA    56       6.975  13.635   1.677  1.00  0.00              
ATOM    130  CA  ALA    56       7.860  13.759   2.852  1.00  0.00              
ATOM    131  C   ALA    56       7.062  13.663   4.162  1.00  0.00              
ATOM    132  O   ALA    56       7.440  12.923   5.062  1.00  0.00              
ATOM    133  N   GLY    57       5.946  14.374   4.257  1.00  0.00              
ATOM    134  CA  GLY    57       5.066  14.313   5.423  1.00  0.00              
ATOM    135  C   GLY    57       4.608  12.890   5.687  1.00  0.00              
ATOM    136  O   GLY    57       4.614  12.421   6.830  1.00  0.00              
ATOM    137  N   ALA    58       4.217  12.185   4.621  1.00  0.00              
ATOM    138  CA  ALA    58       3.755  10.803   4.736  1.00  0.00              
ATOM    139  C   ALA    58       4.818   9.838   5.239  1.00  0.00              
ATOM    140  O   ALA    58       4.564   9.054   6.159  1.00  0.00              
ATOM    141  N   ARG    59       6.008   9.886   4.650  1.00  0.00              
ATOM    142  CA  ARG    59       7.091   9.014   5.075  1.00  0.00              
ATOM    143  C   ARG    59       7.493   9.346   6.521  1.00  0.00              
ATOM    144  O   ARG    59       7.801   8.433   7.280  1.00  0.00              
ATOM    145  N   ARG    60       7.450  10.612   6.885  1.00  0.00              
ATOM    146  CA  ARG    60       7.751  11.037   8.260  1.00  0.00              
ATOM    147  C   ARG    60       6.811  10.380   9.266  1.00  0.00              
ATOM    148  O   ARG    60       7.263   9.759  10.239  1.00  0.00              
ATOM    149  N   LEU    61       5.503  10.468   9.001  1.00  0.00              
ATOM    150  CA  LEU    61       4.489   9.867   9.836  1.00  0.00              
ATOM    151  C   LEU    61       4.663   8.345   9.917  1.00  0.00              
ATOM    152  O   LEU    61       4.571   7.760  10.999  1.00  0.00              
ATOM    153  N   LEU    62       4.893   7.704   8.774  1.00  0.00              
ATOM    154  CA  LEU    62       5.056   6.264   8.755  1.00  0.00              
ATOM    155  C   LEU    62       6.311   5.853   9.544  1.00  0.00              
ATOM    156  O   LEU    62       6.227   4.927  10.374  1.00  0.00              
ATOM    157  N   THR    63       7.428   6.529   9.286  1.00  0.00              
ATOM    158  CA  THR    63       8.702   6.263   9.975  1.00  0.00              
ATOM    159  C   THR    63       8.521   6.404  11.490  1.00  0.00              
ATOM    160  O   THR    63       9.002   5.553  12.269  1.00  0.00              
ATOM    161  N   ASP    64       7.825   7.464  11.896  1.00  0.00              
ATOM    162  CA  ASP    64       7.587   7.754  13.318  1.00  0.00              
ATOM    163  C   ASP    64       6.707   6.740  14.007  1.00  0.00              
ATOM    164  O   ASP    64       6.641   6.725  15.242  1.00  0.00              
ATOM    165  N   ALA    65       5.993   5.914  13.238  1.00  0.00              
ATOM    166  CA  ALA    65       5.153   4.868  13.784  1.00  0.00              
ATOM    167  C   ALA    65       5.643   3.462  13.469  1.00  0.00              
ATOM    168  O   ALA    65       4.946   2.485  13.721  1.00  0.00              
ATOM    169  N   GLY    66       6.854   3.363  12.922  1.00  0.00              
ATOM    170  CA  GLY    66       7.481   2.086  12.640  1.00  0.00              
ATOM    171  C   GLY    66       6.910   1.290  11.478  1.00  0.00              
ATOM    172  O   GLY    66       6.994   0.074  11.476  1.00  0.00              
ATOM    173  N   LEU    67       6.294   1.974  10.511  1.00  0.00              
ATOM    174  CA  LEU    67       5.719   1.312   9.336  1.00  0.00              
ATOM    175  C   LEU    67       6.624   1.518   8.132  1.00  0.00              
ATOM    176  O   LEU    67       7.219   2.593   7.986  1.00  0.00              
ATOM    177  N   ALA    68       6.719   0.524   7.245  1.00  0.00              
ATOM    178  CA  ALA    68       6.083  -0.792   7.394  1.00  0.00              
ATOM    179  C   ALA    68       6.764  -1.591   8.503  1.00  0.00              
ATOM    180  O   ALA    68       7.949  -1.413   8.731  1.00  0.00              
ATOM    181  N   HIS    69       5.994  -2.445   9.155  1.00  0.00              
ATOM    182  CA  HIS    69       6.432  -3.119  10.377  1.00  0.00              
ATOM    183  C   HIS    69       7.490  -4.162  10.098  1.00  0.00              
ATOM    184  O   HIS    69       7.387  -4.961   9.162  1.00  0.00              
END
